def setUp(self):
        datadir = get_data_dir()

        self.infile = datadir + "test.fasta"
        self.outfile = datadir + "test_temp.txt"
    #    args = parser.parse_args(["-h"])

        self.BLAST = runBLAST(self.infile, self.outfile)
Exemple #2
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#    file_name = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/test.fasta"
#    file_name = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/test_blastx.fasta"
    outfile = "/home/sw167/Postdoc/Project_Fungi/data/test_out.txt"
    #    args = parser.parse_args(["-h"])

    file_name = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All.fas"
    outfile = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All_130202.out"

    args = parser.parse_args([file_name, outfile])
#    args = parser.parse_args()


#    main(args)


    BLAST = runBLAST(args.file_name, args.outfile)
#    BLAST.run()
#    BLAST.custom_Update()
#    BLAST.check2()
    taxa_list_file = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All_130202.out.Taxa_67Genes"
    outfile = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All_130202.out.Seqs_67genes"

    taxa_file = open(taxa_list_file, "r")
    efetch_taxa_list = pickle.load(taxa_file)
    exist_ref_seq_list = open("/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Eurotio_alltaxa.list", "r")
#        infile = open(file_name, "r")

    efetch_taxa_set = set()
    for taxa in efetch_taxa_list:
        taxa = taxa.lower()
        efetch_taxa_set.add(taxa)